This notebook plots breakdowns of Germany transmission lineages over time (using only the assignment on the MCC trees).
Number of genomes collected each day, coloured by the time since the age of the transmission lineage when the genome was collected (time from the oldest sampled genome in the lineage to the sampling time of the genome). Note that only genomes in transmission lineages are shown (no singletons).
Number of genomes collected each day, coloured by the TMRCA of the transmission lineage. Note that only genomes in transmission lineages are shown (no singletons).
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
The weekly sampling frequency of the 8 largest r state transmission lineages.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
Lineage size breakdown of Germany genomes collected each week. The 8 largest lineages are coloured.
## Error in maptools::unionSpatialPolygons(cp, attr[, region]): isTRUE(gpclibPermitStatus()) is not TRUE
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'match': object 'germany.f' not found
Lineage size breakdown of Germany genomes collected each week.
Lineage size breakdown of Germany genomes collected each week.
Lineage size breakdown of Germany genomes collected each week.
Lineage size breakdown of Germany genomes collected each week.
## Warning in xy.coords(x, y, xlabel, ylabel, log): 21 y values <= 0 omitted from
## logarithmic plot
Lineage size breakdown of Germany genomes collected each week.
Lineage size breakdown of Germany genomes collected each week.
Lineage size breakdown of Germany genomes collected each week.
Illustration of the time course of the 50 largest Dusseldorf transmission lineages in our dataset. Each row is a transmission lineage. Dots are genome sampling times and boxes show the range of sampling times for each transmission lineage (sampling duration). Asterisks show the TMRCA of each lineage. On the right, n indicates the number of Dusseldorf genomes in the lineage and the duration of lineage detection (time between the lineage’s oldest and most recent genomes). Sampling times of the first 500 SARS-CoV-2 genomes collected in the Dusseldorf have been obscured.
| cluster | Pango.lineage | sample_date | lineage_seqs | state |
|---|---|---|---|---|
| LIN-Germany-B.1.1.7-23859-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-22 | 2718 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-23859-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-22 | 2718 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-26624-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-31 | 2575 | Saxony |
| LIN-Germany-B.1.1.7-34110-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-18 | 1983 | Baden-Wurttemberg |
| LIN-Germany-B.1.1.7-29629-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-25 | 1646 | Thuringia |
| LIN-Germany-B.1.1.7-34109-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-22 | 1556 | Thuringia |
| LIN-Germany-B.1.1.7-7290-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-02 | 1468 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-24120-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-25 | 1296 | Rhineland-Palatinate |
| LIN-Germany-B.1.1.7-31690-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-05 | 922 | Thuringia |
| LIN-Germany-B.1.1.7-31690-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-05 | 922 | Thuringia |
| LIN-Germany-B.1.1.7-31690-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-05 | 922 | Bavaria |
| LIN-Germany-B.1.1.7-31690-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-05 | 922 | Thuringia |
| LIN-Germany-B.1.1.7-55470-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-22 | 767 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-33946-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-08 | 635 | Bavaria |
| LIN-Germany-B.1.1.7-35161-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-19 | 608 | Saxony |
| LIN-Germany-B.1.1.7-25980-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-09 | 577 | Saxony |
| LIN-Germany-B.1.1.7-63701-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-11 | 520 | Berlin |
| LIN-Germany-B.1.1.7-9569-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-09 | 518 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-27729-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-27 | 517 | Thuringia |
| LIN-Germany-B.1.1.7-9106-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-28 | 478 | Baden-Wurttemberg |
| LIN-Germany-B.1.1.7-38045-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-27 | 438 | Rhineland-Palatinate |
| LIN-Germany-B.1.1.7-38114-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-14 | 432 | Baden-Wurttemberg |
| LIN-Germany-B.1.1.7-35231-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-09 | 430 | |
| LIN-Germany-B.1.1.7-39671-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-08 | 426 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-38575-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-17 | 415 | Berlin |
| LIN-Germany-B.1.160-20210602_DTA_MCC_1029 | B.1.160 | 2020-11-13 | 378 | Saarland |
| LIN-Germany-B.1.1.7-54961-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-09 | 336 | Bremen |
| LIN-Germany-B.1.1.7-54961-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-09 | 336 | Bremen |
| LIN-Germany-B.1.1.7-32894-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-24 | 314 | Thuringia |
| LIN-Germany-B.1.1.7-32894-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-24 | 314 | Thuringia |
| LIN-Germany-B.1.1.7-32894-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-24 | 314 | Thuringia |
| LIN-Germany-B.1.1.7-33722-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-12 | 313 | Saxony-Anhalt |
| LIN-Germany-B.1.1.7-33722-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-12 | 313 | Saxony-Anhalt |
| LIN-Germany-B.1.1.7-59513-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-13 | 280 | Bavaria |
| LIN-Germany-B.1.1.317-20210602_DTA_MCC_38 | B.1.1.317 | 2021-01-07 | 274 | Bavaria |
| LIN-Germany-B.1.1.7-30660-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-26 | 274 | Rhineland-Palatinate |
| LIN-Germany-B.1.1.7-30660-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-26 | 274 | Saxony |
| LIN-Germany-B.1.1.7-18644-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-18 | 259 | Lower Saxony |
| LIN-Germany-B.1.1.7-27635-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-22 | 243 | Saxony-Anhalt |
| LIN-Germany-B.1.1.7-27635-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-22 | 243 | |
| LIN-Germany-B.1.1.7-23525-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-29 | 231 | Bavaria |
| LIN-Germany-B.1.1.7-23525-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-29 | 231 | Bavaria |
| LIN-Germany-B.1.1.7-23525-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-29 | 231 | Bavaria |
| LIN-Germany-B.1.221-20210602_DTA_MCC_4 | B.1.221.2 | 2020-03-21 | 229 | Saarland |
| LIN-Germany-B.1.1.7-64316-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-16 | 223 | North Rhine-Westphalia |
| LIN-Germany-B.1.221-20210602_DTA_MCC_306 | B.1.221 | 2020-10-17 | 222 | Saarland |
| LIN-Germany-B.1.221-20210602_DTA_MCC_306 | B.1.221 | 2020-10-17 | 222 | Saarland |
| LIN-Germany-B.1.1.7-40790-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-13 | 210 | Bremen |
| LIN-Germany-B.1.1.7-40790-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-13 | 210 | Bremen |
| LIN-Germany-B.1.1.7-40790-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-13 | 210 | Bremen |
| LIN-Germany-B.1.351-20210602_DTA_MCC_1624 | B.1.351 | 2021-02-04 | 205 | Saarland |
| LIN-Germany-B.1.351-20210602_DTA_MCC_1624 | B.1.351 | 2021-02-04 | 205 | Saarland |
| LIN-Germany-B.1.1.7-54346-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-08 | 191 | Baden-Wurttemberg |
| LIN-Germany-B.1.1.7-60099-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-25 | 188 | Thuringia |
| LIN-Germany-B.1.1.7-17101-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-19 | 186 | Hamburg |
| LIN-Germany-B.1.1.7-17101-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-19 | 186 | Hamburg |
| LIN-Germany-B.1.1.7-53110-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-05 | 183 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-53110-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-05 | 183 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-53110-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-05 | 183 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-62408-20210602_DTA_MCC_1 | B.1.1.7 | 2021-01-21 | 173 | Hesse |
| LIN-Germany-B.1.1.7-26692-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-27 | 170 | Baden-Wurttemberg |
| LIN-Germany-A-20210602_DTA_MCC_68 | A | 2020-03-14 | 144 | Hamburg |
| LIN-Germany-B.1.1.317-20210602_DTA_MCC_63 | B.1.1.317 | 2021-01-22 | 142 | Bavaria |
| LIN-Germany-B.1.1.7-4662-20210602_DTA_MCC_1 | B.1.1.7 | 2021-02-19 | 142 | Thuringia |
| LIN-Germany-B.1.1.7-36198-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-02 | 139 | Baden-Wurttemberg |
| LIN-Germany-B.1.221-20210602_DTA_MCC_920 | B.1.221 | 2020-10-01 | 139 | Saarland |
| LIN-Germany-B.1.1.7-2546-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-26 | 136 | North Rhine-Westphalia |
| LIN-Germany-B.1.1.7-8475-20210602_DTA_MCC_1 | B.1.1.7 | 2021-03-04 | 131 | North Rhine-Westphalia |
| LIN-Germany-B.1.221-20210602_DTA_MCC_90 | B.1.221 | 2020-10-19 | 131 | Saarland |
Illustration of the time course of the 50 earliest Dusseldorf transmission lineages in our dataset. Each row is a transmission lineage. Dots are genome sampling times and boxes show the range of sampling times for each transmission lineage (sampling duration). Asterisks show the TMRCA of each lineage. On the right, n indicates the number of Dusseldorf genomes in the lineage and the duration of lineage detection (time between the lineage’s oldest and most recent genomes). Sampling times of the first 500 SARS-CoV-2 genomes collected in the Dusseldorf have been obscured.
Illustration of the time course of the 50 most recent (by TMRCA) Dusseldorf transmission lineages in our dataset. Each row is a transmission lineage. Dots are genome sampling times and boxes show the range of sampling times for each transmission lineage (sampling duration). Asterisks show the TMRCA of each lineage. On the right, n indicates the number of Dusseldorf genomes in the lineage and the duration of lineage detection (time between the lineage’s oldest and most recent genomes). Sampling times of the first 500 SARS-CoV-2 genomes collected in the Dusseldorf have been obscured.
Illustration of the time course of the 50 Dusseldorf transmission lineages in our dataset with the longest period of cryptic circulation. Each row is a transmission lineage. Dots are genome sampling times and boxes show the range of sampling times for each transmission lineage (sampling duration). Asterisks show the TMRCA of each lineage. On the right, n indicates the number of Dusseldorf genomes in the lineage and the duration of lineage detection (time between the lineage’s oldest and most recent genomes). Sampling times of the first 500 SARS-CoV-2 genomes collected in the Dusseldorf have been obscured.
Illustration of the time course of the 50 Dusseldorf transmission lineages in our dataset with the longest sampling duration (from earliest to most recently collected genome). Each row is a transmission lineage. Dots are genome sampling times and boxes show the range of sampling times for each transmission lineage (sampling duration). Asterisks show the TMRCA of each lineage. On the right, n indicates the number of Dusseldorf genomes in the lineage and the duration of lineage detection (time between the lineage’s oldest and most recent genomes). Sampling times of the first 500 SARS-CoV-2 genomes collected in the Dusseldorf have been obscured.
Illustration of the time course of the 50 Dusseldorf transmission lineages in our dataset with the longest unobserved period before reemerging. Each row is a transmission lineage. Dots are genome sampling times and boxes show the range of sampling times for each transmission lineage (sampling duration). Asterisks show the TMRCA of each lineage. On the right, n indicates the number of Dusseldorf genomes in the lineage and the duration of lineage detection (time between the lineage’s oldest and most recent genomes). Sampling times of the first 500 SARS-CoV-2 genomes collected in the Dusseldorf have been obscured.
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-conda-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)
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## Matrix products: default
## BLAS/LAPACK: /home/hforoughmand/miniconda3/envs/r4-base/lib/libopenblasp-r0.3.12.so
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## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] maptools_1.1-1 colorspace_2.0-0 raster_3.4-13 sp_1.4-5
## [5] viridis_0.5.1 viridisLite_0.3.0 stringr_1.4.0 knitr_1.31
## [9] gplots_3.1.1 plyr_1.8.6 phytools_0.7-70 maps_3.3.0
## [13] ggtree_2.4.1 ggsci_2.9 ggplot2_3.3.3 treeio_1.14.3
## [17] rjson_0.2.20 beastio_0.3.3 tidytree_0.3.3 ape_5.4-1
## [21] lubridate_1.7.10 dplyr_1.0.5 tictoc_1.0
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## loaded via a namespace (and not attached):
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## [4] tmvnsim_1.0-2 gtools_3.8.2 bslib_0.2.4
## [7] expm_0.999-6 BiocManager_1.30.12 rvcheck_0.1.8
## [10] highr_0.8 yaml_2.2.1 numDeriv_2016.8-1.1
## [13] pillar_1.5.1 lattice_0.20-41 glue_1.4.2
## [16] quadprog_1.5-8 phangorn_2.6.2 digest_0.6.27
## [19] RColorBrewer_1.1-2 htmltools_0.5.1.1 Matrix_1.3-2
## [22] pkgconfig_2.0.3 purrr_0.3.4 patchwork_1.1.1
## [25] scales_1.1.1 tibble_3.1.0 combinat_0.0-8
## [28] generics_0.1.0 ellipsis_0.3.2 withr_2.4.1
## [31] lazyeval_0.2.2 mnormt_2.0.2 magrittr_2.0.1
## [34] crayon_1.4.1 evaluate_0.14 fansi_0.4.2
## [37] nlme_3.1-152 MASS_7.3-53.1 foreign_0.8-81
## [40] tools_4.0.3 lifecycle_1.0.0 aplot_0.0.6
## [43] munsell_0.5.0 plotrix_3.8-1 jquerylib_0.1.3
## [46] compiler_4.0.3 clusterGeneration_1.3.7 caTools_1.18.2
## [49] tinytex_0.31 rlang_0.4.10 grid_4.0.3
## [52] igraph_1.2.6 bitops_1.0-6 rmarkdown_2.7
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## [61] KernSmooth_2.23-18 stringi_1.5.3 Rcpp_1.0.6
## [64] vctrs_0.3.8 scatterplot3d_0.3-41 tidyselect_1.1.0
## [67] xfun_0.22 coda_0.19-4